Charge Imbalance for a case in Resonance Structure Generation

xiaoruiDong / RDMC

Reaction Data and Molecular Conformers (RDMC) is a package dealing with reactions, molecules, conformers, majorly in 3D.

https://xiaoruidong.github.io/RDMC/

MIT License

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Charge Imbalance for a case in Resonance Structure Generation #84

Open xiaoruiDong opened 4 months ago

xiaoruiDong commented 4 months ago

CCC(CC=C(N)[O])C(=[NH2+])[O-]

When generating resonance structures for this molecule, there are 12 entries, while RMG predicts 6 entries. The extra 6 entries are molecules with +1 charge. Need to check how these molecules are generated and why they are not being filtered out.

xiaoruiDong commented 4 months ago

Update: generating from its neutral resonance structure CCC(CC=C(N)[O])C(N)=O results in the correct resonance structures. The initial formal charge may screw up something.